eas.bib

% References. First version from:
% https://github.com/katyhuff/2016-06-19-dagstuhl/blob/gh-pages/dagstuhl-manifesto.bib

@inproceedings{mcconahy2012techniques,
  title={Techniques for monitoring runtime architectures of socio-technical ecosystems},
  author={McConahy, A and Eisenbraun, Ben and Howison, James and Herbsleb, James D and Sliz, P},
  booktitle={Workshop on Data-Intensive Collaboration in Science and Engineering (CSCW 2012)},
  year={2012},
  url = {http://www.dicose.org/images/5/5d/Mcconahy_eisenbraun_howison_herbsleb.pdf}
}

@article{howison2015understanding,
  title={Understanding the scientific software ecosystem and its impact: Current and future measures},
  author={Howison, James and Deelman, Ewa and McLennan, Michael J. and da Silva, Rafael Ferreira and Herbsleb, James D},
  journal={Research Evaluation},
  pages={rvv014},
  year={2015},
  publisher={Oxford University Press},
  doi = {10.1093/reseval/rvv014}
}

@article{howison2014collaboration,
  title={Collaboration Through Open Superposition: A Theory of the Open Source Way.},
  author={Howison, James and Crowston, Kevin},
  journal={{MIS} Quarterly},
  volume={38},
  number={1},
  pages={29--50},
  year={2014},
  url = {http://aisel.aisnet.org/cgi/viewcontent.cgi?article=3156&context=misq}
}

@article{DBLP:journals/scp/MensBK14,
  author    = {Kim Mens and
               M. G. J. van den Brand and
               Holger M. Kienle},
  title     = {Guest editors' introduction to the 4th issue of Experimental Software
               and Toolkits {(EST-4)}},
  journal   = {Sci. Comput. Program.},
  volume    = {79},
  pages     = {1--5},
  year      = {2014},
  url       = {http://dx.doi.org/10.1016/j.scico.2012.12.005},
  doi       = {10.1016/j.scico.2012.12.005},
  timestamp = {Tue, 29 Oct 2013 10:53:14 +0100},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/scp/MensBK14},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}

@article{NOWAKOWSKI2011608,
title = "The Collage Authoring Environment",
journal = "Procedia Computer Science",
volume = "4",
number = "",
pages = "608 - 617",
year = "2011",
note = "",
issn = "1877-0509",
author = "Piotr Nowakowski and Eryk Ciepiela and Daniel Harezlak and Joanna Kocot and Marek Kasztelnik and Tomasz Bartynski and Jan Meizner and Grzegorz Dyk and Maciej Malawski",
}

@misc{execpapers,
  author = {Peter Sloot},
  title = {The Executable Paper Grand Challenge},
  year = {2011},
  publisher = {Elsevier},
  note = {http://www.executablepapers.com/about-challenge.html},
}s

@inproceedings{DBLP:journals/procedia/GorpM11,
  author    = {Pieter Van Gorp and
               Steffen Mazanek},
  title     = {{SHARE:} a web portal for creating and sharing executable research
               papers},
  booktitle = {Proceedings of the International Conference on Computational Science,
               {ICCS} 2011},
  pages     = {589--597},
  year      = {2011},
  month = Jun
}

@inproceedings{senyard2004have,
  title={How to have a successful free software project},
  author={Senyard, Anthony and Michlmayr, Martin},
  booktitle={Software Engineering Conference, 2004. 11th Asia-Pacific},
  url={http://www.cyrius.com/publications/senyard_michlmayr-successful_project.pdf},
  pages={84--91},
  year={2004},
  organization={IEEE}
}

@misc{onto_soft_what_2016,
	title = {What is a {Geoscience} {Paper} of the {Future} {\textbar} {The} {Geoscience} {Papers} of the {Future} {Initiative}},
	url = {http://www.ontosoft.org/gpf/what-is-a-gpf},
	urldate = {2016-06-24},
	journal = {http://www.ontosoft.org/gpf/what-is-a-gpf},
	author = {{OntoSoft}},
	year = {2016},
	file = {What is a Geoscience Paper of the Future | The Geoscience Papers of the Future Initiative:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/35QZ2GP4/what-is-a-gpf.html:text/html}
}

@misc{barba_reproducibility_2012,
	title = {Reproducibility {PI} {Manifesto}},
	url = {https://figshare.com/articles/Reproducibility_PI_Manifesto/104539},
	abstract = {Slides for lightning talk at the ICERM workshop on "Reproducibility in Computational and Experimental Mathematics", December 2012.
Shared under CC-BY.},
	urldate = {2016-06-24},
	author = {Barba, Lorena A.},
	month = dec,
	year = {2012},
	note = {DOI:10.6084/m9.figshare.104539.v1},
	keywords = {open science, reproducibility},
	file = {Figshare Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/E3R8XPPP/104539.html:text/html;Full Text (HTML):/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/3RDIWAA8/m9.figshare.104539.html:text/html}
}

@misc{rse_conference_2016_ukrse_2016,
	title = {{UKRSE} {Objectives}},
	url = {http://www.rse.ac.uk/objectives.html},
	urldate = {2016-06-24},
	journal = {UKRSE Objectives},
	author = {{Research Software Engineers Association (UKRSE)}},
	year = {2013},
	file = {Objectives:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/EEHQ4CR7/objectives.html:text/html}
}

@misc{rse_conference_2016_what_2016,
	title = {What is a {Research} {Software} {Engineer}?},
	url = {http://www.rse.ac.uk/who.html},
	urldate = {2016-06-24},
	author = {{Research Software Engineers Association (UKRSE)}},
	year = {2013},
	file = {What is a Research Software Engineer?:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/PQTZVU28/who.html:text/html}
}

@article{weiner_astronomical_2009,
	title = {Astronomical {Software} {Wants} {To} {Be} {Free}: {A} {Manifesto}},
	shorttitle = {Astronomical {Software} {Wants} {To} {Be} {Free}},
	url = {http://arxiv.org/abs/0903.3971},
	abstract = {Astronomical software is now a fact of daily life for all hands-on members of our community. Purpose-built software for data reduction and modeling tasks becomes ever more critical as we handle larger amounts of data and simulations. However, the writing of astronomical software is unglamorous, the rewards are not always clear, and there are structural disincentives to releasing software publicly and to embedding it in the scientific literature, which can lead to significant duplication of effort and an incomplete scientific record. We identify some of these structural disincentives and suggest a variety of approaches to address them, with the goals of raising the quality of astronomical software, improving the lot of scientist-authors, and providing benefits to the entire community, analogous to the benefits provided by open access to large survey and simulation datasets. Our aim is to open a conversation on how to move forward. We advocate that: (1) the astronomical community consider software as an integral and fundable part of facility construction and science programs; (2) that software release be considered as integral to the open and reproducible scientific process as are publication and data release; (3) that we adopt technologies and repositories for releasing and collaboration on software that have worked for open-source software; (4) that we seek structural incentives to make the release of software and related publications easier for scientist-authors; (5) that we consider new ways of funding the development of grass-roots software; (6) and that we rethink our values to acknowledge that astronomical software development is not just a technical endeavor, but a fundamental part of our scientific practice.},
	urldate = {2016-06-24},
	journal = {arXiv:0903.3971 [astro-ph]},
	author = {Weiner, Benjamin J. and Blanton, Michael R. and Coil, Alison L. and Cooper, Michael C. and Davé, Romeel and Hogg, David W. and Holden, Bradford P. and Jonsson, Patrik and Kassin, Susan A. and Lotz, Jennifer M. and Moustakas, John and Newman, Jeffrey A. and Prochaska, J. X. and Teuben, Peter J. and Tremonti, Christy A. and Willmer, Christopher N. A.},
	month = mar,
	year = {2009},
	note = {arXiv: 0903.3971},
	keywords = {Astrophysics - Instrumentation and Methods for Astrophysics},
	file = {arXiv\:0903.3971 PDF:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/NTGUT9CS/Weiner et al. - 2009 - Astronomical Software Wants To Be Free A Manifest.pdf:application/pdf;arXiv.org Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/W5IZS4VK/0903.html:text/html}
}

@article{aleksic_open_2015,
	title = {An {Open} {Science} {Peer} {Review} {Oath}},
	issn = {2046-1402},
	url = {http://f1000research.com/articles/3-271/v2},
	doi = {10.12688/f1000research.5686.2},
	language = {en},
	urldate = {2016-06-24},
	journal = {F1000Research},
	author = {Aleksic, Jelena and Alexa, Adrian and Attwood, Teresa K and Chue Hong, Neil and Dahlö, Martin and Davey, Robert and Dinkel, Holger and Förstner, Konrad U and Grigorov, Ivo and Hériché, Jean-Karim and Lahti, Leo and MacLean, Dan and Markie, Michael L and Molloy, Jenny and Schneider, Maria Victoria and Scott, Camille and Smith-Unna, Richard and Vieira, Bruno Miguel and {as part of the AllBio: Open Science \& Reproducibility Best Practice Workshop}},
	month = jan,
	year = {2015},
	file = {An Open Science Peer Review Oath - F1000Research:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/2SVQMNNE/v2.html:text/html}
}

@misc{alex_holcombe_open_2011,
	title = {Open {Access} {Pledge} {\textbar} {Making} and tracking open access pledges},
	url = {http://www.openaccesspledge.com/},
	urldate = {2016-06-24},
	author = {{Alex Holcombe}},
	year = {2011},
	file = {Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/JANWK49D/www.openaccesspledge.com.html:text/html}
}

@article{arfon_m._smith_software_2016,
	title = {Software Citation Principles},
	doi = {10.7717/peerj-cs.86},
	journal = {PeerJ Computer Science},
	author = {Arfon M. Smith and Kyle E. Niemeyer and Daniel S. Katz and {FORCE11 Software Citation Working Group}},
	volume={2},
	pages = {e86},
	year = {2016},
}

@misc{nick_barnes_science_2013,
	title = {Science {Code} {Manifesto}},
	copyright = {Copyright 2013 Climate Code Foundation},
	url = {http://sciencecodemanifesto.org/},
	urldate = {2016-06-24},
	author = {{Nick Barnes}},
	year = {2013},
	file = {Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/WAQC5UVC/sciencecodemanifesto.org.html:text/html}
}

@article{becker_karlskrona_2014,
	title = {The {Karlskrona} manifesto for sustainability design},
	url = {http://arxiv.org/abs/1410.6968},
	abstract = {Sustainability is a central concern for our society, and software systems increasingly play a central role in it. As designers of software technology, we cause change and are responsible for the effects of our design choices. We recognize that there is a rapidly increasing awareness of the fundamental need and desire for a more sustainable world, and there is a lot of genuine goodwill. However, this alone will be ineffective unless we come to understand and address our persistent misperceptions. The Karlskrona Manifesto for Sustainability Design aims to initiate a much needed conversation in and beyond the software community by highlighting such perceptions and proposing a set of fundamental principles for sustainability design.},
	urldate = {2016-06-24},
	journal = {arXiv:1410.6968 [cs]},
	author = {Becker, Christoph and Chitchyan, Ruzanna and Duboc, Leticia and Easterbrook, Steve and Mahaux, Martin and Penzenstadler, Birgit and Rodriguez-Navas, Guillermo and Salinesi, Camille and Seyff, Norbert and Venters, Colin and Calero, Coral and Kocak, Sedef Akinli and Betz, Stefanie},
	month = oct,
	year = {2014},
	note = {arXiv: 1410.6968},
	keywords = {Computer Science - General Literature, Computer Science - Software Engineering},
	file = {arXiv\:1410.6968 PDF:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/JZSC64UT/Becker et al. - 2014 - The Karlskrona manifesto for sustainability design.pdf:application/pdf;arXiv\:1410.6968 PDF:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/CGUECC9B/Becker et al. - 2014 - The Karlskrona manifesto for sustainability design.pdf:application/pdf;arXiv.org Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/67QAZZ2J/1410.html:text/html;arXiv.org Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/6UANCACI/1410.html:text/html;Snapshot:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/K9SX9UG2/karlskrona-manifesto.html:text/html}
}

@article{wilkinson_fair_2016,
	title = {The {FAIR} {Guiding} {Principles} for scientific data management and stewardship},
	volume = {3},
	issn = {2052-4463},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792175/},
	doi = {10.1038/sdata.2016.18},
	abstract = {There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.},
	urldate = {2016-06-24},
	journal = {Scientific Data},
	author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Mercè and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J.G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and ’t Hoen, Peter A.C and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
	month = mar,
	year = {2016},
	pmid = {26978244},
	pmcid = {PMC4792175},
	file = {PubMed Central Full Text PDF:/Users/khuff/Library/Application Support/Zotero/Profiles/lvoutoj9.default/zotero/storage/JWBH5P2M/Wilkinson et al. - 2016 - The FAIR Guiding Principles for scientific data ma.pdf:application/pdf}
}

@article{Baker2016,
  title = {Why scientists must share their research code},
  url = {http://www.nature.com/news/why-scientists-must-share-their-research-code-1.20504},
  doi = {10.1038/nature.2016.20504},
  author = {Monya Baker},
  journal = {Nature},
  year = {2016}
}


@article{pan_disciplinary_2016,
	title = {Disciplinary differences of software use and impact in scientific literature},
	issn = {0138-9130, 1588-2861},
	url = {http://link.springer.com/article/10.1007/s11192-016-2138-4},
	doi = {10.1007/s11192-016-2138-4},
	abstract = {Software plays an important role in the advancement of science. Software developers, users, and funding agencies have deep interests in the impact of software on science. This study investigates the use and impact of software by examining how software is mentioned and cited among 9548 articles published in PLOS ONE in 12 defined disciplines. Our results demonstrate that software is widely used in scientific research and a substantial uncitedness of software exists across different disciplines. Findings also show that the practice of software citations varies noticeably at the discipline level and software that is free for academic use is more likely to receive citations than commercial software.},
	language = {en},
	urldate = {2016-11-22},
	journal = {Scientometrics},
	author = {Pan, Xuelian and Yan, Erjia and Hua, Weina},
	month = sep,
	year = {2016},
	pages = {1--18},
	file = {Full Text PDF:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/HMTHZW3J/Pan et al. - 2016 - Disciplinary differences of software use and impac.pdf:application/pdf;Snapshot:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/HKIAJA3P/s11192-016-2138-4.html:text/html}
}

@article{duck_survey_2016,
	title = {A {Survey} of {Bioinformatics} {Database} and {Software} {Usage} through {Mining} the {Literature}},
	volume = {11},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157989},
	doi = {10.1371/journal.pone.0157989},
	abstract = {Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT), though some are instead seeing rapid growth (e.g., the GO, R). We find a striking imbalance in resource usage with the top 5\% of resource names (133 names) accounting for 47\% of total usage, and over 70\% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here:  http://dx.doi.org/10.6084/m9.figshare.1281371 .},
	number = {6},
	urldate = {2016-07-18},
	journal = {PLOS ONE},
	author = {Duck, Geraint and Nenadic, Goran and Filannino, Michele and Brass, Andy and Robertson, David L. and Stevens, Robert},
	month = jun,
	year = {2016},
	keywords = {Bioinformatics, Eigenvectors, Electrocardiography, Gene ontologies, Genomic databases, Genomic medicine, machine learning, Nucleic acids},
	pages = {e0157989},
	file = {Full Text PDF:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/QKAZ8V7S/Duck et al. - 2016 - A Survey of Bioinformatics Database and Software U.pdf:application/pdf;Snapshot:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/QAJMHVH6/article.html:text/html}
}

@article{duck_bionerds:_2013,
	title = {{bioNerDS}: exploring bioinformatics’ database and software use through literature mining},
	volume = {14},
	issn = {1471-2105},
	shorttitle = {{bioNerDS}},
	url = {http://dx.doi.org/10.1186/1471-2105-14-194},
	doi = {10.1186/1471-2105-14-194},
	abstract = {Biology-focused databases and software define bioinformatics and their use is central to computational biology. In such a complex and dynamic field, it is of interest to understand what resources are available, which are used, how much they are used, and for what they are used. While scholarly literature surveys can provide some insights, large-scale computer-based approaches to identify mentions of bioinformatics databases and software from primary literature would automate systematic cataloguing, facilitate the monitoring of usage, and provide the foundations for the recovery of computational methods for analysing biological data, with the long-term aim of identifying best/common practice in different areas of biology.},
	urldate = {2016-07-18},
	journal = {BMC Bioinformatics},
	author = {Duck, Geraint and Nenadic, Goran and Brass, Andy and Robertson, David L. and Stevens, Robert},
	year = {2013},
	pages = {194},
	file = {Full Text PDF:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/4WK9IAAG/Duck et al. - 2013 - bioNerDS exploring bioinformatics’ database and s.pdf:application/pdf;Snapshot:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/QKRABVQX/1471-2105-14-194.html:text/html}
}

@article{pan_assessing_2015,
	title = {Assessing the impact of software on science: {A} bootstrapped learning of software entities in full-text papers},
	volume = {9},
	issn = {1751-1577},
	shorttitle = {Assessing the impact of software on science},
	url = {http://www.sciencedirect.com/science/article/pii/S1751157715300602},
	doi = {10.1016/j.joi.2015.07.012},
	abstract = {Although software has helped researchers conduct research, little is known of the impact of software on science. To fill this gap, this article proposes an improved bootstrapping method to extract software entities from full-text papers and assess their impact on science. Evaluation results show that the proposed entity extraction system outperforms three baseline methods on extracting software entities from full-text papers. The proposed method is then used to learn software entities from all papers published in PLoS ONE in 2014. More than 2000 unique software entities are obtained which accounted for more than 20,000 mentions and more than 7000 citations. The paper finds that software is commonly used in the scientific community along with a substantial uncitedness.},
	number = {4},
	urldate = {2016-05-10},
	journal = {Journal of Informetrics},
	author = {Pan, Xuelian and Yan, Erjia and Wang, Qianqian and Hua, Weina},
	month = oct,
	year = {2015},
	keywords = {Bootstrapping, citation analysis, Entity extraction, Information extraction, software, Software citation},
	pages = {860--871},
	file = {0612.pdf:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/T5ZW5MG2/0612.pdf:application/pdf;ScienceDirect Snapshot:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/R3D526MU/S1751157715300602.html:text/html}
}

@article{howison_software_2015,
	title = {Software in the scientific literature: {Problems} with seeing, finding, and using software mentioned in the biology literature},
	volume = {67},
	issn = {2330-1643},
	shorttitle = {Software in the scientific literature},
	doi = {10.1002/asi.23538},
	language = {en},
	number = {9},
	urldate = {2016-12-01},
	journal = {Journal of the Association for Information Science and Technology},
	author = {Howison, James and Bullard, Julia},
	month = sep,
	year = {2016},
	keywords = {bibliographic citations, biology, journals},
	pages = {2137--2155},
}

@article{momcheva_software_2015,
	title = {Software {Use} in {Astronomy}: an {Informal} {Survey}},
	shorttitle = {Software {Use} in {Astronomy}},
	url = {http://arxiv.org/abs/1507.03989},
	abstract = {We report on an informal survey about the use of software in the worldwide astronomical community. The survey was carried out between December 2014 and February 2015, collecting responses from 1142 astronomers, spanning all career levels. We find that all participants use software in their research. The vast majority of participants, 90\%, write at least some of their own software. Even though writing software is so wide-spread among the survey participants, only 8\% of them report that they have received substantial training in software development. Another 49\% of the participants have received "little" training. The remaining 43\% have received no training. We also find that astronomers' software stack is fairly narrow. The 10 most popular tools among astronomers are (from most to least popular): Python, shell scripting, IDL, C/C++, Fortran, IRAF, spreadsheets, HTML/CSS, SQL and Supermongo. Across all participants the most common programing language is Python (\$67{\textbackslash}pm 2{\textbackslash}\%\$), followed by IDL (\$44{\textbackslash}pm 2{\textbackslash}\%\$), C/C++ (\$37{\textbackslash}pm 2{\textbackslash}\%\$) and Fortran (\$28{\textbackslash}pm 2{\textbackslash}\%\$). IRAF is used frequently by \$24{\textbackslash}pm 1{\textbackslash}\%\$ of participants. We show that all trends are largely independent of career stage, area of research and geographic location.},
	urldate = {2016-11-22},
	journal = {arXiv:1507.03989 [astro-ph]},
	author = {Momcheva, Ivelina and Tollerud, Erik},
	month = jul,
	year = {2015},
	note = {arXiv: 1507.03989},
	keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Computers and Society},
	file = {arXiv\:1507.03989 PDF:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/IZDHR728/Momcheva and Tollerud - 2015 - Software Use in Astronomy an Informal Survey.pdf:application/pdf;arXiv.org Snapshot:/Users/howison/Library/Application Support/Zotero/Profiles/u6jomw7h.default/zotero/storage/X8GDBTT7/1507.html:text/html}
}

@inproceedings{howison_sustaining_2015,
	address = {Irvine, CA},
	title = {Sustaining scientific infrastructures: transitioning from grants to peer production (work-in-progress)},
	copyright = {Copyright 2015 is held by the authors. Copyright permissions, when appropriate, must be obtained directly from the authors.},
	shorttitle = {Sustaining scientific infrastructures},
	url = {https://www.ideals.illinois.edu/handle/2142/73439},
	abstract = {Science now relies on mid-level infrastructure, including shared instruments, cell lines, supercomputing resources, data sets, and software components. These are beyond the facilities and services traditionally provided by individual universities; funding agencies such as the NSF often support their initial creation but their long-term sustainability is a challenge and commercialization is only rarely an option. A promising model, though, is broad-based community support through peer production, often inspired by the organization of open source software projects. Such transitions, though, are not automatic or easy, just as commercialization is not. In this research I am studying successful and unsuccessful attempts to transition, building theory and practical guidance for scientists and funding agencies. In this work-in-progress paper, I present the motivation and background for the study and provide motivation through preliminary description of my first case study.},
	language = {English},
	urldate = {2015-07-30},
	author = {Howison, James},
	month = mar,
	year = {2015}
}

@inproceedings{bietz_sustaining_2012,
	address = {New York, NY, USA},
	series = {{CSCW} '12},
	title = {Sustaining the development of cyberinfrastructure: an organization adapting to change},
	isbn = {978-1-4503-1086-4},
	shorttitle = {Sustaining the development of cyberinfrastructure},
	url = {http://doi.acm.org.ezproxy.lib.utexas.edu/10.1145/2145204.2145339},
	doi = {10.1145/2145204.2145339},
	abstract = {Cyberinfrastructures are virtual organizations comprised of people and large-scale scientific computational infrastructures. Cyberinfrastructures endeavor to support "cutting-edge" science and must continually evolve and be under development in order to maintain their relevance and usefulness. This qualitative study of a cyberinfrastructure development project to support the new science of metagenomics investigates how sustaining cyberinfrastructure entails continually realigning the relationships among people, technologies, and organizations.},
	urldate = {2012-05-30},
	booktitle = {Proceedings of the {ACM} 2012 conference on {Computer} {Supported} {Cooperative} {Work}},
	publisher = {ACM},
	author = {Bietz, Matthew J. and Ferro, Toni and Lee, Charlotte P.},
	year = {2012},
	keywords = {Cyberinfrastructure, e-science, Infrastructure, organizations, sustainability, Synergizing},
	pages = {901--910}
}

@misc{sustaining-research-projects,
title={A guide to sustainability models for research software projects},
author={Daniel S. Katz and C. Titus Brown and Arfon M. Smith and Adam Slagell},
url={https://github.com/danielskatz/sustaining-research-projects},
year={2016},
note={[Last accessed: 2016-11-22]}
}

@article{jay_git_jors,
	title = {{“Not everyone can use Git”: Research Software Engineers’ recommendations for scientist-centred software support (and what researchers really think of them)}},
	journal = {Journal of Open Research Software},
	author = {Caroline Jay and Rawan Sanyour and Robert Haines},
  year = {In press}
}

@inproceedings{desouza_2014,
  title={{Defining sustainability through developers’ eyes: Recommendations from an interview study}},
  author={M\'{a}rio Rosado de Souza and Robert Haines and Caroline Jay},
  year={2014},
  booktitle={WSSSPE 2},
  url={http://dx.doi.org/10.6084/m9.figshare.1111925},
  doi={10.6084/m9.figshare.1111925}
}